fix: extend atomic writes to parser, reporter, and experiment outputs

Applies atomic_write_json to the remaining final pipeline outputs that
were still using plain write_json:

- core/reporter.py: pipeline_output.json (final report, ensure_ascii=False)
- core/parser_adapter.py: dataset.json and analyzer_output.json (parse
  outputs consumed by subsequent expensive LLM stages)
- experiment.py: experiment results (legacy direct-run path)

Skipped: checkpoint files (designed for incremental writes),
scanner intermediate state, and the diff_filter sidecar report
(cheap to regenerate, not consumed downstream).

Author: joshbouncesecurity

libs/openant-core/core/parser_adapter.py

@@ -18,6 +18,7 @@
 from pathlib import Path
 
 from core.schemas import ParseResult
+from utilities.atomic_io import atomic_write_json
 from utilities.file_io import open_utf8, read_json, write_json
 
 # Root of openant-core (where parsers/ lives)
@@ -173,7 +174,7 @@ def _maybe_apply_diff_filter(
 
     stats = apply_diff_filter(units, manifest)
 
-    write_json(result.dataset_path, dataset)
+    atomic_write_json(result.dataset_path, dataset)
     # Expose stats on the ParseResult via a side-channel file; the parse
     # step_context reads this when assembling parse.report.json.
     diff_report_path = os.path.join(output_dir, "diff_filter.report.json")
@@ -363,8 +364,8 @@ def _parse_python(repo_path: str, output_dir: str, processing_level: str, skip_t
         dataset = _apply_reachability_filter(dataset, output_dir, processing_level)
 
     # Write outputs
-    write_json(dataset_path, dataset)
-    write_json(analyzer_output_path, analyzer_output)
+    atomic_write_json(dataset_path, dataset)
+    atomic_write_json(analyzer_output_path, analyzer_output)
     units_count = len(dataset.get("units", []))
     print(f"  Python parser complete: {units_count} units", file=sys.stderr)
 

libs/openant-core/core/reporter.py

@@ -19,6 +19,7 @@
 from pathlib import Path
 
 from core.schemas import ReportResult
+from utilities.atomic_io import atomic_write_json
 from utilities.file_io import open_utf8, read_json, write_json
 
 # Root of openant-core
@@ -367,7 +368,7 @@ def build_pipeline_output(
         print(_banner, file=sys.stderr)
 
     os.makedirs(os.path.dirname(os.path.abspath(output_path)), exist_ok=True)
-    write_json(output_path, pipeline_output, ensure_ascii=False)
+    atomic_write_json(output_path, pipeline_output, ensure_ascii=False)
     print(f"  pipeline_output.json: {len(findings_data)} findings", file=sys.stderr)
     print(f"  Written to {output_path}", file=sys.stderr)
 

libs/openant-core/experiment.py

@@ -35,6 +35,7 @@
 from pathlib import Path
 
 from utilities.llm_client import AnthropicClient, get_global_tracker
+from utilities.atomic_io import atomic_write_json
 from utilities.file_io import read_json, write_json
 from prompts.prompt_selector import get_analysis_prompt
 from prompts.vulnerability_analysis import get_system_prompt as get_stage1_system_prompt
@@ -1033,7 +1034,7 @@ def main():
         suffix = "" if args.no_enhanced else "_enhanced"
         output_path = f"experiment_{args.dataset}_{args.model}{suffix}_{datetime.now().strftime('%Y%m%d_%H%M%S')}.json"
 
-    write_json(output_path, experiment)
+    atomic_write_json(output_path, experiment)
     print()
     print(f"Results saved to: {output_path}")